Enumerating soil biodiversity

Proceedings of the National Academy of Sciences, Год журнала: 2023, Номер 120(33)

Опубликована: Авг. 7, 2023

Soil is an immense habitat for diverse organisms across the tree of life, but just how many live in soil surprisingly unknown. Previous efforts to enumerate biodiversity consider only certain types (e.g., animals) or report values groups without partitioning species that versus other habitats. Here, we reviewed literature show likely home 59 ± 15% on Earth. We therefore estimate approximately two times greater than previous estimates, and include representatives from simplest (microbial) most complex (mammals) organisms. Enchytraeidae have greatest percentage (98.6%), followed by fungi (90%), Plantae (85.5%), Isoptera (84.2%). Our results demonstrate biodiverse singular habitat. By using this biodiversity, can more accurately quantitatively advocate organismal conservation restoration as a central goal Anthropocene.

Язык: Английский

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Shifting microbial communities can enhance tree tolerance to changing climates

Science, Год журнала: 2023, Номер 380(6647), С. 835 - 840

Опубликована: Май 25, 2023

Climate change is pushing species outside of their evolved tolerances. Plant populations must acclimate, adapt, or migrate to avoid extinction. However, because plants associate with diverse microbial communities that shape phenotypes, shifts in associations may provide an alternative source climate tolerance. Here, we show tree seedlings inoculated sourced from drier, warmer, colder sites displayed higher survival when faced drought, heat, cold stress, respectively. Microbially mediated drought tolerance was associated increased diversity arbuscular mycorrhizal fungi, whereas lower fungal richness, likely reflecting a reduced burden nonadapted taxa. Understanding microbially enhance our ability predict and manage the adaptability forest ecosystems changing climates.

Язык: Английский

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ITS alchemy: On the use of ITS as a DNA marker in fungal ecology

Fungal ecology, Год журнала: 2023, Номер 65, С. 101274 - 101274

Опубликована: Июль 26, 2023

High throughput sequencing of PCR amplicons derived from environmental DNA (aka metabarcoding) has become an integral part fungal ecology, enabling in-depth characterization communities. In most cases, the rDNA Internal Transcribed Spacer (ITS) region, which a long history as target in systematics, is used barcode marker. Despite improvements techniques and bioinformatics approaches, there are inherent limitations associated with use single-locus marker that often ignored. this text, I discuss both biological methodological ITS For example, proper species delimitation not possible single marker, significant barcoding gap (i.e. interspecific divergence) missing between sister taxa ITS. Further, we can rarely be fully confident about assigned species-level taxonomy based on available reference sequences. addition to limitations, extra layer complexity variation blended into metabarcoding data due errors may look similar natural molecular variation. The processing must take account basic properties well generated biases. regard, cannot adopt approaches settings other markers, such 16S 18S, blindly. intraspecific variability sometimes intragenomic variability, sequences clustered approach level resolution community studies. Therefore, argue concept amplicon sequence variants (ASVs) applicable. Although region by far best option general (meta)barcoding for fungi, contribution meant remind against naive or simplistic stimulating further discussions.

Язык: Английский

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Environmental DNA/RNA for pathogen and parasite detection, surveillance, and ecology

Trends in Parasitology, Год журнала: 2023, Номер 39(4), С. 285 - 304

Опубликована: Фев. 8, 2023

Язык: Английский

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Towards exhaustive community ecology via DNA metabarcoding

Molecular Ecology, Год журнала: 2023, Номер 32(23), С. 6320 - 6329

Опубликована: Фев. 10, 2023

Abstract Exhaustive biodiversity data, covering all the taxa in an environment, would be fundamental to understand how global changes influence organisms living at different trophic levels, and evaluate impacts on interspecific interactions. Molecular approaches such as DNA metabarcoding are boosting our ability perform inventories. Nevertheless, even though a few studies have recently attempted exhaustive reconstructions of communities, holistic assessments remain rare. The majority published last years used just one or two markers analysed limited number taxonomic groups. Here, we provide overview emerging that can allow all‐taxa biological by combining large specific primers, exploiting power universal primers obtain good information key while limiting overlooked biodiversity. Multiplexes shotgun sequencing capture enrichment may better coverage compared standard metabarcoding, but still require major methodological advances. identify strengths limitations approaches, suggest new development lines might improve broad scale analyses near future. More ecological communities greatly increase value studies, improving understanding consequences ongoing environmental multiple components

Язык: Английский

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Pervasive associations between dark septate endophytic fungi with tree root and soil microbiomes across Europe

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Янв. 2, 2024

Abstract Trees interact with a multitude of microbes through their roots and root symbionts such as mycorrhizal fungi endophytes. Here, we explore the role fungal predictors soil root-associated microbiomes widespread broad-leaved trees across European latitudinal gradient. Our results suggest that, alongside factors climate, soil, vegetation properties, colonization by ectomycorrhizal, arbuscular mycorrhizal, dark septate endophytic also shapes tree-associated microbiomes. Notably, structure our sites is more strongly consistently associated endophyte than many abiotic factors. Root endophytes has consistent negative association relative abundance diversity nutrient cycling genes. study not only indicates that root-symbiotic interactions are an important factor structuring communities functions in forest ecosystems, but hitherto less studied likely to be central players these interactions.

Язык: Английский

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Fungal community composition predicts forest carbon storage at a continental scale

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Март 16, 2024

Abstract Forest soils harbor hyper-diverse microbial communities which fundamentally regulate carbon and nutrient cycling across the globe. Directly testing hypotheses on how microbiome diversity is linked to forest storage has been difficult, due a lack of paired data in situ observations accumulation storage. Here, we investigated relationship between soil microbiomes 238 inventory plots spanning 15 European countries. We show that composition fungal, but not bacterial, species tightly coupled both biotic conditions seven-fold variation tree growth rates biomass stocks when controlling for effects dominant type, climate, other environmental factors. This linkage particularly strong symbiotic endophytic ectomycorrhizal fungi known directly facilitate growth. Since this system are closely positively correlated with belowground stocks, conclude fungal predictor overall continent.

Язык: Английский

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Fungal biodeterioration and preservation of cultural heritage, artwork, and historical artifacts: extremophily and adaptation

Microbiology and Molecular Biology Reviews, Год журнала: 2024, Номер 88(1)

Опубликована: Янв. 5, 2024

SUMMARYFungi are ubiquitous and important biosphere inhabitants, their abilities to decompose, degrade, otherwise transform a massive range of organic inorganic substances, including plant matter, rocks, minerals, underpin major significance as biodeteriogens in the built environment cultural heritage. Fungi often most obvious agents heritage biodeterioration with effects ranging from discoloration, staining, biofouling destruction building components, historical artifacts, artwork. Sporulation, morphological adaptations, explorative penetrative lifestyle filamentous fungi enable efficient dispersal colonization solid substrates, while many species able withstand environmental stress factors such desiccation, ultra-violet radiation, salinity, potentially toxic substances. Many can grow under nutrient-limited conditions, produce resistant cell forms that survive through long periods adverse conditions. The fungal chemoorganotrophic metabolism therefore adaptation success frequently encountered extremophilic conditions associated indoor outdoor Apart free-living fungi, lichens growth form pioneer colonizers materials, especially stone- mineral-based components. This article surveys roles heritage, reference mechanisms involved relation substances encountered, well methods by which be assessed combated, how certain processes may utilized bioprotection.

Язык: Английский

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Environmental DNA: The next chapter

Molecular Ecology, Год журнала: 2024, Номер 33(11)

Опубликована: Апрель 16, 2024

Abstract Molecular tools are an indispensable part of ecology and biodiversity sciences implemented across all biomes. About a decade ago, the use implementation environmental DNA (eDNA) to detect signals extracted from samples opened new avenues research. Initial eDNA research focused on understanding population dynamics target species. Its scope thereafter broadened, uncovering previously unrecorded via metabarcoding in both well‐studied understudied ecosystems taxonomic groups. The application rapidly became established research, field by its own. Here, we revisit key expectations made land‐mark special issue Ecology 2012 frame development six areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour environment (6) reference database development. We pinpoint success eDNA, yet also discuss shortfalls not met, highlighting areas priority identify unexpected developments. In parallel, our retrospective couples screening peer‐reviewed literature with survey users including academics, end‐users commercial providers, which address focus efforts advance eDNA. With rapid ever‐increasing pace technical advances, future looks bright, successful applications best practices must become more interdisciplinary reach full potential. Our retrospect gives towards concretely moving forward.

Язык: Английский

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A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses

Molecular Ecology Resources, Год журнала: 2023, Номер 24(5)

Опубликована: Авг. 7, 2023

Abstract Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through require sophisticated processing of high‐throughput sequencing data from taxonomically informative barcodes. Various sets universal and taxon‐specific primers have been developed, extending the usability across archaea, bacteria eukaryotes. Accordingly, multitude analysis tools pipelines also developed. Often, several developed workflows are designed to process same amplicon data, making it somewhat puzzling choose one among plethora existing pipelines. each pipeline its own specific philosophy, strengths limitations, which should be considered depending on aims any study, well bioinformatics expertise user. In this review, we outline input requirements, supported operating systems particular attributes thirty‐two with goal helping users select their projects.

Язык: Английский

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